Post-translational modifications—including phosphorylation, acetylation, and ubiquitination—allow for the fine-tuning of signaling pathways and networks within cells. Mass spectrometry-based proteomics techniques are powerful tools for the investigation of these networks. Dynamic protein phosphorylation is a key cellular regulatory mechanism, and the characterization of global phosphorylation profiles using large-scale proteomic approaches, including antibody-based phosphopeptide enrichment, has proven informative. Acetylation has also been studied using these approaches, and as histone deacetylase inhibitors gain clinical importance, the need to better characterize their mechanism of action has accelerated lysine acetylation proteomics research. Further, ubiquitination is gaining increased attention as an important mechanism for both signal transduction and proteolytic degradation. Most recently, new ubiquitin affinity reagents, such as the ubiquitin remnant antibody, have become available, allowing for the identification of hundreds of ubiquitinylated lysine residues in human cells.